Published July 28, 2021 | Version v1
Dataset Open

Molecular trajectories and general MD files: Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal

  • 1. Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
  • 2. Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
  • 3. Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
  • 4. Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.

Description

This repository includes the MD simulation dataset of self-assembled ionic liquid crystal reported in the article of Sci. Adv. 7, eabf0669 (2021) [DOI: 10.1126/sciadv.abf0669]. The chemical structure of ionic liquid crystal is described in Fig. 1A. The cation involves an ionic moiety of N-methyl-N,N,N-triethylammonium group, and the terminals of the two alkyl chains are conjugated dienes. The anion is tetrafluoroborate BF4. The molecular and atomic-group charges of cation and anion are shown in the topology files named "ilc-oplsdft.itp" and "bf4-oplsdft.itp", respectively.  The TIP3P and TIP4P/2005 models are employed for water molecules. After the careful equilibration process, the production MD was performed for 50 ns under the NPT condition at each composition.  This dataset provides the configuration, topology, and general MD input files of Gromacs for all the states and models of bicontinuous and columnar structures obtained in the article.  The 3D view of bicontinuous and columnar structures can be available in Fig. 2. The attached edr and log files are energy and general outputs of the MD simulation generated in our environment, and the xtc file is a trajectory output generated with a time interval of 20 ps.

Notes

This work is supported by JSPS KAKENHI Numbers JP19H05715, JP19H05718, JP20H02058, and JP20K15108 from the Japan Society for the Promotion of Science, and by the Elements Strategy Initiative for Catalysts and Batteries Number JPMXP0112101003. The simulations were performed by using the supercomputers of Hokkaido University (Grand Chariot), Research Center for Computational Science at Okazaki, Osaka University (OCTOPUS), and Kyushu University (ITO) partially through the HPCI System Research Project (Project IDs: hp200043, hp200055, hp200065, and hp200120).

Files

OPLS-DFT-TIP3P.zip

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Additional details

Related works

Is supplement to
Journal article: 10.1126/sciadv.abf0669 (DOI)